A new low temperature biochemically compatible bonding technique using fluoropolymers has been developed in this work and characterized in terms of mechanical bonding strength and biochemical resistance. This bonding technique uses a spin-on Teflon-like amorphous fluorocarbon polymer (CYTOPTM) as a bonding interface layer. The developed bonding process requires a bonding temperature of 160 °C and the bonding strength attained from the process shows 4.3 Mpa in silicon-to-silicon. Furthermore, the bonding technique achieves reliable and leak-proof bonding in various substrates and provides excellent chemical resistance and biocompatibility for some specific immunoassays. The bonding technique developed in this work has been successfully applied to the development of a microfluidic motherboard system with surface mountable microfluidic components.